First-principles Quantum Chemical Calculations Research Articles

First-principle quantum-chemical calculations of several thermomechanical parameters of beryllium ceramics

The first-principle quantum-chemical calculations of elastic constants for beryllium oxide and their approximation (the Voigt-Reuss-Hill model) for a polycrystalline material are used to derive quantitative estimates of several thermomechanical parameters of BeO ceramics: isothermal compression coefficient, sound velocity, the Debye temperature, and coefficients of linear and volume temperature expansion, as well as the temperature dependence of molar heat capacity and thermal conductivity. The results are discussed in correlation to available experimental data.

Theoretical Design of Optical Switches Using the Spin Transition Phenomenon

The spin characteristics of octahedrically coordinated Fe(II) compounds are determined from first-principles quantum chemical calculations. Four novel Fe(II) spin transition materials are suggested for use in optical switching applications.

Adhesion Mechanism of Metal Impurities on Si Wafers in Alkali Solution

First-principles quantum chemical calculations have been performed to reveal the adhesion mechanisms of metal impurities (Al or Fe) onto the Si wafer surface in alkali solution. As typical hydroxyl complexes of these metals, or are used in computation. The lowest energy paths of the adhesion reaction have been obtained for the respective complex when the Si surface is terminated with OH groups and develops into a hydrophilic condition. The potential energy changes along these reaction paths were evaluated and the probabilities of the metal adhesion were compared. The detaching mechanism was also investigated for Al or Fe hydroxyl complex compounds in which a water molecule attacks the Si-O or O-metal bond at the interface between the complex and the surface. The results are discussed in comparison with recent experimental findings. © 2004 The Electrochemical Society. All rights reserved.

Polycyclic aromates on close-packed metal surfaces: functionalization, molecular chemisorption and organic epitaxy

In this paper we present a detailed analysis of the molecular mechanisms of perylene and PTCDA bonding to two close-packed noble metal surfaces, Ag(111) and Au(111), with the aim of elucidating the relation between bonding and interface structure. Our analysis is based on a combination of high-resolution electron energy-loss spectroscopy and first-principles quantum chemical calculations (density functional theory) of molecular orbitals and vibrations. Experimentally, the key observation is the activation of certain totally symmetric modes by symmetry breaking at the surface. Analysing calculated vibrational eigenvectors and the induced dynamic distortions of the lowest unoccupied molecular orbital in detail, we propose an interaction model according to which the central carbon ring in both molecules constitutes the molecular chemisorption centre. In the case of perylene, its reactivity is rather small. By the application of functional groups to the aromatic backbone, however, the reactivity can be tuned over a wide range, leading to a dramatic enhancement of the molecule–substrate interaction in the case of PTCDA/Ag(111), as testified by the remarkable interface epitaxy. The example of the weakly interacting PTCDA/Au(111) interface illustrates the limitations of the present scheme of chemisorption strength engineering. Finally, the implications of our results for a detailed determination of the adsorption site are discussed.

Mechanism of a chemical classic: quantum chemical investigation of the autocatalyzed reaction of the serendipitous wöhler synthesis of urea.

The detailed reaction pathways for the ammonium cyanate transformation into urea (Wöhler's reaction) in the gas phase, in solution, and in the solid state have exhaustively been explored by means of first-principles quantum chemical calculations at the B3LYP level of theory using the 6-31G(d,p) basis set. This serendipitous synthesis of urea is predicted to proceed in two steps; the first step involves the decomposition of the ammonium cyanate to ammonia and isocyanic or cyanic acid, and the second one, which is the main reaction step (and probably the rate-determining step), involves the interaction of NH(3) with either isocyanic or cyanic acid. Several alternative pathways were envisaged for the main reaction step of Wöhler's reaction in a vacuum involving the formation of "four-center" transition states. Modeling Wöhler's reaction in aqueous solution and in the solid state, it was found that the addition of NH(3) to both acids is assisted (autocatalyzed) by the active participation of extra H(2)O and/or NH(3) molecules, through a preassociative, cooperative, and hydrogen-transfer relay mechanism involving the formation of "six-center" or even "eight-center" transition states. The most energetically economic path of the rate-determining step of Wöhler's reaction is that of the addition of NH(3) to the C=N double bond of isocyanic acid, directly affording urea. An alternative pathway corresponding to the anti-addition of ammonia to the Ctbd1;N triple bond of cyanic acid, yielding urea's tautomer HN=C(OH)NH(2), seems to be another possibility. In the last case, urea is formed through a prototropic tautomerization of its enolic form. The energies of the reactants, products, and all intermediates along with the barrier heights for each reaction path have been calculated at the B3LYP/6-31G(d,p) level of theory. The geometry optimization and characterization of all of the stationary points found on the potential energy hypersurfaces was performed at the same level of theory.

Silanone(Si=O)on Si(100): intermediate for initial silicon oxidation

Infrared-absorption measurements and first-principles quantum chemical calculations reveal that the initial oxidation of clean $\mathrm{Si}(100)\ensuremath{-}(2\ifmmode\times\else\texttimes\fi{}1)$ by ${\mathrm{O}}_{2}$ involves the formation of a metastable silanone intermediate, $(\mathrm{O})\mathrm{Si}=\mathrm{O},$ containing two oxygen atoms presumably from the same ${\mathrm{O}}_{2}$ molecule. Oxygen insertion into the surface silicon Si-Si backbonds is either thermally activated (\ensuremath{\sim}1-eV barrier) or induced by atomic hydrogen exposure with formation of novel dihydride intermediates.

Vibrational identification of the surface reaction intermediates for the dehalogenation of trichloroethene on PdCu(1 1 0) alloy

The adsorption and dissociation of trichloroethene (TCE) on PdCu(1 1 0) have been investigated under the view of high resolution electron energy loss spectroscopy (HREELS) and first-principle quantum chemical calculations. At 180 K and after an exposure of 10 L, TCE is physisorbed on the surface. The HREELS spectrum is similar to the gas-phase one, measured by infrared spectroscopy. There are small shifts in the bands of the HREELS spectrum, which also indicate a weak interaction between the molecule and the surface. The chemistry of the TCE dissociation on PdCu(1 1 0) is more complex than the one on Cu(1 1 0). By increasing the surface temperature, a great variety of surface species occurs, as shown by the experimental spectra and confirmed by the calculations. This reaction seems to occur relatively early, at 200 K. At 280 K most of the CCl bonds have been already broken. The decrease of the intensity of the νCCl stretching vibration and the increase of the intensity of the metalCl vibration are shown to be fingerprints of this process.

The effect of network topology on proton trapping in amorphous SiO/sub 2/

We report the results of first-principles quantum chemical calculations of the interactions of H/H/sup +/ with oxide ring structures of varying sizes. The calculations suggest that the binding and stability of protons in amorphous SiO/sub 2/ depend upon the topology of the interacting network. A neutral hydrogen atom, H/sup 0/, does not bind to bridging O atoms in the rings, but may occupy voids within larger rings.

Nucleation site of Cu on the H-terminated Si(111) surface

First-principles quantum chemical calculations have been performed to clarify the nucleation site of Cu on the H-terminated Si(111) surface. The adhesion energies of a Cu atom on various sites have been obtained accurately. We have examined the following surface species as candidates for the Cu nucleation site: Si dihydride and monohydride species, fluoride, chloride, and hydroxide species, and locally oxidized sites. The basis set for Cu, which is one of the transition metals, has been chosen suitably. Results of our calculation indicate that (1) a Cu atom migrates freely on the H-terminated Si(111) surface, (2) it adheres selectively on the OH-terminated site, which is considered to exist mainly at a kink site and at the intersection of step edges, and (3) the Cu atom adhering on the OH-terminated site easily grows to a cluster.

Mechanism of electron trapping in Ge-doped SiO2 glass

We present a possible mechanism of electron trapping in Ge-doped SiO2 glass on the basis of first-principles quantum chemical calculations on clusters of atoms modeling the local structures in the glassy system. The calculations suggest that the so-called “Ge(1) and Ge(2)” centers are distinctly different electron centers rather than GeO4− variants and that an electron trapped at an oxygen vacancy site is a promising candidate for Ge(2).

First Computational Evidence for a Catalytic Bridging Hydroxide Ion in a Phosphodiesterase Active Site

Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulates the intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding the structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it is uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand is theoretically determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.

A First Principles Analysis of C−H Bond Formation in Ethylene Hydrogenation

The Horiuti−Polanyi mechanism for ethylene hydrogenation over Pd(111) is examined using first-principle density functional quantum chemical calculations. Cluster and periodic slab DFT-GGA calculations were carried out to determine the modes and energies of chemisorption for a sequence of proposed intermediates, along with overall reaction energies and activation barriers for each of the speculated elementary steps. The DFT-calculated binding energies for ethylene (π), ethylene (di-σ), ethyl, vinyl, ethylidyne, atomic oxygen, and atomic carbon on the Pd19 cluster (and the Pd(111) slab) were found to be −30 (−27), −60 (−62), −130 (−140), −237 (−254), −620 (−636), −375 (−400), and −610 (−635) kJ/mol. The slab results were found to be within 20 kJ/mol of the cluster results. Frequency calculations along with predicted chemisorption energies indicate that ethylene adsorbs in both π- and di-σ-configurations. At moderate temperatures, the binding energies for π- and di-σ-bound ethylene are comparable. At low sur...

Interpretation of sulphur 2p XPS spectra in sulfide minerals by means ofab initio calculations

First-principles quantum chemical calculations have been used to reproduce S 2p x-ray photoelectron spectroscopy binding energies for a number of sulphide minerals where accurate experimental data are available. Periodic calculations have been performed with the Hartree–Fock/density functional hybrid method B3LYP. Reasonable agreement between the calculated and experimentally observed S 2p3/2 binding energies was achieved for the sulphides sphalerite, wurtzite, pyrite, galena and chalcopyrite. Based on these periodic calculations simple pseudo-hydrogen-saturated cluster models were constructed that give reliable predictions for the spectra of all reference compounds, while also allowing for the treatment of more complex sulphide and polysulphide structures inaccessible to present periodic approaches. Copyright © 2000 John Wiley & Sons, Ltd.

Predicting lateral surface interactions through density functional theory: application to oxygen on Rh(100)

First-principle density functional quantum chemical calculations are used to predict the binding energies and lateral interactions of adsorbed atomic oxygen on Rh(100). The DFT results are subsequently used to parameterize two general models for the a priori prediction of adsorbate interactions on surfaces. The first model is based on pairwise interactions where the lateral effects are assumed to be additive. The second model is based on bond-order conservation (BOC) principles. The parameters for these models are determined by performing a series of DFT calculations on Rh cluster and slab models of the Rh(100) surface. Rh(8,3), Rh(9,4), and Rh(12,17) clusters are used to determine the O/Rh(100) binding energy and lateral interaction energies for different adsorbate–surface configurations. The O/Rh(100) binding energy on the Rh(100) surface is calculated to be 117±5kcal/mol. Lateral interactions involving metal atom sharing are repulsive, ranging from 2 to 7kcal/mol per oxygen on a pairwise additive basis for both clusters as well as extended surfaces. We develop and analyze pairwise additive and bond-order conservation models for use in predicting lateral interaction energies. An unaltered BOC approach is found to overestimate the interaction energies. However, a modified BOC approach in which the basic interactions are scaled against DFT predictions proved to be significantly better in its predictions. Comparison of the modified BOC model with experiments suggests that this is a viable mean for predicting lateral interaction energies.

Reaction of HF molecules with metal impurities on Si surfaces

First-principles quantum chemical calculations have been performed to reveal the reaction mechanisms of HF molecules with metal impurities (Al or Cu) on Si surfaces. The lowest energy paths of this HF attack reaction have been obtained in two situations when a metal atom adheres to a Si surface with and without an O atom incorporated between the metal atom and the surface. The potential energy changes along these reaction paths were evaluated. It was revealed that a HF molecule has the ability to etch an Al monoxide on the Si surface. On the other hand, HF is not effective in the etching of a metal atom (Al or Cu) which has directly bonded to a Si surface.

First-principles analysis of the hydrogenation of carbon monoxide over palladium

The reaction paths for the hydrogenation of CO to methanol over Pdx (x = 1–4 and 19) cluster models were examined using first-principle density functional quantum chemical calculations. The predicted adsorption energies for the most favorable binding modes for CO, H2, HCO, H3CO, CH3OH, C, O and H on a Pd19 model Pd(111) clusters were -147, -62, -340, -51, -195, -33, -610, -349 and -251 kJ/mol, respectively. The most favorable modes for CO, CH3O, H, C and O on Pd(111) were all found to be the 3-fold fcc site. The most favorable modes for the formyl and formaldehyde surface intermediates at low coverage were the 3-fold (ζ2µ3), and the di-σ sites, respectively. At higher surface coverages, however, the atop ζ1 (C) and the π modes for the formyl and formaldehyde intermediates were more likely. The computed adsorption energies were subsequently used to compute overall reaction energies for the hydrogenation of CO to methanol. The initial hydrogenation of CO to the ζ1 (C) HCO intermediate was found to be +52 kJ/mol endothermic and has been speculated as a possible rate-limiting step. The remaining surface hydrogenation steps become increasingly more exothermic as more hydrogen was added. The elementary steps of formyl to formaldehyde, formaldehyde to methoxide and methoxide to methanol were computed to be -9, -26 and -33 kJ/mol, respectively. The overall energy for CO dissociation was found to be highly unlikely at +260 kJ/mol and a clear indication that methanation and chain growth chemistry is not very likely over Pd. The most favorable reaction coordinate for the hydrogenation of CO to the ζ1 (C) formyl intermediate was that which proceeds over a single Pd site where there is a migratory insertion of the CO into a Pd–H bond. The barrier for this path was computed to be +78 kJ/mol on the Pd19 cluster. There was a very weak dependence on cluster size. This is a likely indication that this reaction is structure insensitive. A second path which involved the coupling of H and CO over a bridge site was found to be +130 kJ/mol which is less likely, but may also occur under different conditions.

Reaction coordinate analyses of transition metal catalyzed C [sbnd]H and C [sbnd]S activation steps

The application of first-principle quantum chemical calculations toward analyzing and understanding heterogeneously catalyzed C X bond activation is reviewed. More specifically, two industrially relevant systems, methane activation and thiophene desulfurization are discussed. Density functional theoretical (DFT) calculations are used to examine C H activation of acetate a precursor to acetate decar☐ylation and C S activation of thiophene. Both systems require a sufficient cluster size model for the catalyst in order to predict energetic information, and hence model periodic trends. C H activation of acetate closely mimics the activation of methane. The reaction path is characterized by a late transition state with respect to the C H bond stretch. There is considerable M H and M C bond formation. The predicted barrier is +115 kJ/mol. Thiophene hydrodesulfurization which occurs via η1 adsorption of thiophene, is initially activated by hydrogenating thiophene to 2,5 dihydrothiophene (DHT). DHT activation proceeds via a metal atom insertion into the C S bond. The formation of an additional M S bond (two-fold sulfur) stabilizes the metallocycle intermediate and lowers the barrier of DHT C S bond breaking from +250 to +150 kJ/mol.